The wettability and filtration efficiency of multi-walled carbon nanotubes (MWCNT) under irradiation with Ar+ ions with an energy of 100 keV have been investigated. Energy dispersive X-ray spectroscopy, Raman spectroscopy, and scanning electron microscopy were used to study the residual manganese content in the filter, as well as to study the structure of irradiated MWCNTs. High fluence irradiated MWCNT (HR-MWCNT) filters showed an improvement in Mn removal of up to 99.6% at a Mn concentration of 10 ppm. HR-MWCNT based filters are extremely hydrophilic, with a 66° wetting angle and high absorption capacity. The efficiency of manganese removal from an aqueous medium has been studied as a function of pH, initial concentration, and mass of MWCNT.